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Shinn EJ, Tajkhorshid E. Generating Concentration Gradients across Membranes for Molecular Dynamics Simulations of Periodic Systems. Int J Mol Sci 2024; 25:3616. [PMID: 38612428 PMCID: PMC11012027 DOI: 10.3390/ijms25073616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/15/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
The plasma membrane forms the boundary between a living entity and its environment and acts as a barrier to permeation and flow of substances. Several computational means of calculating permeability have been implemented for molecular dynamics (MD) simulations-based approaches. Except for double bilayer systems, most permeability studies have been performed under equilibrium conditions, in large part due to the challenges associated with creating concentration gradients in simulations utilizing periodic boundary conditions. To enhance the scientific understanding of permeation and complement the existing computational means of characterizing membrane permeability, we developed a non-equilibrium method that enables the generation and maintenance of steady-state gradients in MD simulations. We utilize PBCs advantageously by imposing a directional bias to the motion of permeants so that their crossing of the boundary replenishes the gradient, like a previous study on ions. Under these conditions, a net flow of permeants across membranes may be observed to determine bulk permeability by a direct application of J=PΔc. In the present study, we explore the results of its application to an exemplary O2 and POPC bilayer system, demonstrating accurate and precise permeability measurements. In addition, we illustrate the impact of permeant concentration and the choice of thermostat on the permeability. Moreover, we demonstrate that energetics of permeation can be closely examined by the dissipation of the gradient across the membrane to gain nuanced insights into the thermodynamics of permeability.
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Affiliation(s)
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Resource Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;
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2
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Subczynski WK, Widomska J, Stein N, Swartz HM. Factors determining barrier properties to oxygen transport across model and cell plasma membranes based on EPR spin-label oximetry. APPLIED MAGNETIC RESONANCE 2021; 52:1237-1260. [PMID: 36267674 PMCID: PMC9581439 DOI: 10.1007/s00723-021-01412-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 07/23/2021] [Accepted: 08/04/2021] [Indexed: 06/01/2023]
Abstract
This review is motivated by the exciting new area of radiation therapy using a phenomenon termed FLASH in which oxygen is thought to have a central role. Well-established principles of radiation biology and physics suggest that if oxygen has a strong role, it should be the level at the DNA. The key aspect discussed is the rate of oxygen diffusion. If oxygen freely diffuses into cells and rapidly equilibrates, then measurements in the extracellular compartment would enable FLASH to be investigated using existing methodologies that can readily measure oxygen in the extracellular compartment. EPR spin-label oximetry allows evaluation of the oxygen permeability coefficient across lipid bilayer membranes. It is established that simple fluid phase lipid bilayers are not barriers to oxygen transport. However, further investigations indicate that many physical and chemical (compositional) factor can significantly decrease this permeation. In biological cell plasma membranes, the lipid bilayer forms the matrix in which integral membrane proteins are immersed, changing organization and properties of the lipid matrix. To evaluate oxygen permeability coefficients across these complex membranes, oxygen permeation across all membrane domains and components must be considered. In this review, we consider many of the factors that affect (decrease) oxygen permeation across cell plasma membranes. Finally, we address the question, can the plasma membrane of the cell form a barrier to the free diffusion of oxygen into the cell interior? If there is a barrier then this must be considered in the investigations of the role of oxygen in FLASH.
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Affiliation(s)
- Witold K. Subczynski
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Justyna Widomska
- Department of Biophysics, Medical University of Lublin, Jaczewskiego 4, Lublin, Poland
| | - Natalia Stein
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Harold M. Swartz
- Department of Radiology, The Geisel School of Medicine at Dartmouth, Lebanon, NH 03766, USA
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3
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Angles G, Hail A, Dotson RJ, Pias SC. Atomistic simulations modify interpretation of spin-label oximetry data. Part 1: intensified water-lipid interfacial resistances. APPLIED MAGNETIC RESONANCE 2021; 52:1261-1289. [PMID: 37292189 PMCID: PMC10249954 DOI: 10.1007/s00723-021-01398-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 06/10/2023]
Abstract
The role of membrane cholesterol in cellular function and dysfunction has been the subject of much inquiry. A few studies have suggested that cholesterol may slow oxygen diffusive transport, altering membrane physical properties and reducing oxygen permeability. The primary experimental technique used in recent years to study membrane oxygen transport is saturation-recovery electron paramagnetic resonance (EPR) oximetry, using spin-label probes targeted to specific regions of a lipid bilayer. The technique has been used, in particular, to assess the influence of cholesterol on oxygen transport and membrane permeability. The reliability of such EPR recordings at the water-lipid interface near the phospholipid headgroups has been challenged by all-atom molecular dynamics (MD) simulation data that show substantive agreement with spin-label probe measurements throughout much of the bilayer. This work uses further MD simulations, with an updated oxygen model, to determine the location of the maximum resistance to permeation and the rate-limiting barrier to oxygen permeation in 1-palmitoyl,2-oleoylphosphatidylcholine (POPC) and POPC/cholesterol bilayers at 25 and 35°C. The current simulations show a spike of resistance to permeation in the headgroup region that was not detected by EPR but was predicted in early theoretical work by Diamond and Katz. Published experimental nuclear magnetic resonance (NMR) oxygen measurements provide key validation of the MD models and indicate that the positions and relative magnitudes of the phosphatidylcholine resistance peaks are accurate. Consideration of the headgroup-region resistances predicts bilayer permeability coefficients lower than estimated in EPR studies, giving permeabilities lower than the permeability of unstirred water layers of the same thickness. Here, the permeability of POPC at 35°C is estimated to be 13 cm/s, compared with 10 cm/s for POPC/cholesterol and 118 cm/s for simulation water layers of similar thickness. The value for POPC is 12 times lower than estimated from EPR measurements, while the value for POPC/cholesterol is 5 times lower. These findings underscore the value of atomic resolution models for guiding the interpretation of experimental probe-based measurements.
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Affiliation(s)
| | | | | | - Sally C. Pias
- Corresponding author: , Department of Chemistry, New Mexico Institute of Mining and Technology (New Mexico Tech), 801 Leroy Place, Socorro, NM 87801, USA
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4
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Dotson RJ, McClenahan E, Pias SC. Updated Evaluation of Cholesterol's Influence on Membrane Oxygen Permeability. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1269:23-30. [PMID: 33966190 DOI: 10.1007/978-3-030-48238-1_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
There is a surprising gap in knowledge regarding the mechanism of oxygen (O2) diffusional delivery at the level of tissues and cells. Yet, the effectiveness of tumor radiotherapy, the success of tissue engineering, and healthy metabolism all require ample intracellular oxygen. Tissue-level diffusion takes place in a complex and crowded macromolecular environment. Cholesterol-rich cellular membranes have been thought to reduce oxygen flux. Here, we use atomistic molecular dynamics simulations to update prior estimates of bilayer permeability and related parameters for 1-palmitoyl,2-oleoylphosphatidylcholine (POPC) and POPC/cholesterol bilayers, using a modified O2 model with improved membrane-water partitioning behavior. This work estimates an oxygen permeability coefficient of 15 ± 1 cm/s for POPC and 11.5 ± 0.4 cm/s for POPC/cholesterol (1:1 molecular ratio) at 37 °C. The permeability of POPC is found to be ~1/3 that of a water layer of similar thickness, and the permeability of POPC/cholesterol is estimated to be 20-30% below that of POPC. Void pathway visualization and free energy data support channeling of oxygen toward the center of cholesterol-incorporating membranes, while partition coefficient data suggest reduced membrane solubility of oxygen due to cholesterol. Further study is needed to understand whether diffusion pathway changes due to cholesterol and other molecular compositional factors influence oxygen availability within tissue.
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Affiliation(s)
- Rachel J Dotson
- Department of Chemistry, New Mexico Institute of Mining and Technology (New Mexico Tech), Socorro, NM, USA
| | - Emily McClenahan
- Department of Chemistry, New Mexico Institute of Mining and Technology (New Mexico Tech), Socorro, NM, USA
| | - Sally C Pias
- Department of Chemistry, New Mexico Institute of Mining and Technology (New Mexico Tech), Socorro, NM, USA.
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5
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Pias SC. How does oxygen diffuse from capillaries to tissue mitochondria? Barriers and pathways. J Physiol 2020; 599:1769-1782. [PMID: 33215707 DOI: 10.1113/jp278815] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 11/11/2020] [Indexed: 12/17/2022] Open
Abstract
Timely delivery of oxygen (O2 ) to tissue mitochondria is so essential that elaborate circulatory systems have evolved to minimize diffusion distances within tissue. Yet, knowledge is surprisingly limited regarding the diffusion pathway between blood capillaries and tissue mitochondria. An established and growing body of work examines the influence cellular and extracellular structures may have on subcellular oxygen availability. This brief review discusses the physiological and pathophysiological significance of oxygen availability, highlights recent computer modelling studies of transport at the cell-membrane level, and considers alternative diffusion pathways within tissue. Experimental and computer modelling studies suggest that oxygen diffusion may be accelerated by cellular lipids, relative to cytosolic and interstitial fluids. Such acceleration, or 'channelling', would occur due to greatly enhanced oxygen solubility in lipids, especially near the midplane of lipid bilayers. Rapid long-range movement would be promoted by anisotropically enhanced lateral diffusion of oxygen along the midplane and by junctions holding lipid structures in close proximity to one another throughout the tissue. Clarifying the biophysical mechanism of oxygen transport within tissue will shed light on limitations and opportunities in tumour radiotherapy and tissue engineering.
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Affiliation(s)
- Sally C Pias
- Department of Chemistry, New Mexico Institute of Mining and Technology (New Mexico Tech), Socorro, NM, USA
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6
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Pias SC. Pathways of Oxygen Diffusion in Cells and Tissues : Hydrophobic Channeling via Networked Lipids. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1232:183-190. [PMID: 31893409 DOI: 10.1007/978-3-030-34461-0_23] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Oxygen delivery to tissue mitochondria relies on simple diffusion in the target cells and tissues. As such, intracellular availability of O2 in tissue depends on its solubility and diffusivity in complex and heterogeneous macromolecular environments. The path of oxygen diffusion is key to its rate of transfer, especially where pathways of differing favorability are present. Most commonly, aqueous media, such as interstitial fluid and cytoplasm, are assumed to provide the dominant diffusion path. Here, the 'hydrophobic channeling' hypothesis is revisited, and several lines of evidence pointing toward lipid-accelerated oxygen diffusion pathways are discussed. The implications of hydrophobic channeling are considered in light of extended membrane networks in cells and tissues.
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Affiliation(s)
- Sally C Pias
- Department of Chemistry, New Mexico Institute of Mining and Technology (New Mexico Tech), Socorro, NM, USA.
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7
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Zhao X, Huang Y, Yuan G, Zuo K, Huang Y, Chen J, Li J, Xue J. A novel tumor and mitochondria dual-targeted photosensitizer showing ultra-efficient photodynamic anticancer activities. Chem Commun (Camb) 2019; 55:866-869. [PMID: 30601489 DOI: 10.1039/c8cc09456j] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We designed and synthesized a simple, but highly effective photosensitizer (G-Mito-Pc), which can precisely target the mitochondria of epidermal growth factor receptor (EGFR)-overexpressing cancer cells, to achieve dual targeting function at both cell and organelle levels in cancer therapy. We further explored the possible molecular mechanism of the enhanced bioactivity of G-Mito-Pc compared to that of the reference photosensitizer using molecular dynamics simulations on their interactions with a physiologically relevant mitochondrial membrane model.
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Affiliation(s)
- Xuan Zhao
- College of Chemistry, National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou, China.
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8
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Oxygen distribution in the fluid/gel phases of lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:879-886. [PMID: 30716292 DOI: 10.1016/j.bbamem.2019.01.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 01/25/2023]
Abstract
The interactions between oxygen and lipid membranes play fundamental roles in basic biological processes (e.g., cellular respiration). Obviously, membrane oxidation is expected to be critically dependent on the distribution and concentration of oxygen in the membrane. Here, we combined theoretical and experimental methods to investigate oxygen partition and distribution in lipid membranes of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) in a temperature range between 298 and 323 K, specifically focusing on the changes caused by the lipid phase and phase transition. Even though oxygen is known to be more concentrated in the center of fluid phase membranes than on the headgroup regions, the distribution profile of oxygen inside gel-phase bilayers remained to be determined. Molecular dynamics simulations now show that the distribution of oxygen inside DPPC bilayers dramatically changes upon crossing the main transition temperature, with oxygen being nearly depleted halfway from the headgroups to the membrane center below the transition temperature. In a parallel approach, singlet oxygen luminescence emission measurements employing the photosensitizer Pheophorbide-a (Pheo) confirmed the differences in oxygen distribution and concentration profiles between gel- and fluid-phase membranes, revealing changes in the microenvironment of the embedded photosensitizer. Our results also reveal that excited triplet state lifetime, as it can be determined from the singlet oxygen luminescence kinetics, is a useful probe to assess oxygen distribution in lipid membranes with distinct lipid compositions.
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9
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Möller MN, Denicola A. Diffusion of nitric oxide and oxygen in lipoproteins and membranes studied by pyrene fluorescence quenching. Free Radic Biol Med 2018; 128:137-143. [PMID: 29673655 DOI: 10.1016/j.freeradbiomed.2018.04.553] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/05/2018] [Accepted: 04/13/2018] [Indexed: 10/17/2022]
Abstract
Oxygen and nitric oxide are small hydrophobic molecules that usually need to diffuse a considerable distance to accomplish their biological functions and necessarily need to traverse several lipid membranes. Different methods have been used to study the diffusion of these molecules in membranes and herein we focus in the quenching of fluorescence of pyrenes inserted in the membrane. The pyrene derivatives have long fluorescence lifetimes (around 200 ns) that make them very sensitive to fluorescence quenching by nitric oxide, oxygen and other paramagnetic species. Results show that the apparent diffusion coefficients in membranes are similar to those in water, indicating that diffusion of these molecules in membranes is not considerably limited by the lipids. This high apparent diffusion in membranes is a consequence of both a favorable partition of these molecules in the hydrophobic interior of membranes and a high diffusion coefficient. Altering the composition of the membrane results in slight changes in diffusion, indicating that in most cases the lipid membranes will not hinder the passage of oxygen or nitric oxide. The diffusion of nitric oxide in the lipid core of low density lipoprotein is also very high, supporting its role as an antioxidant. In contrast to the high permeability of membranes to nitric oxide and oxygen, the permeability to other reactive species such as hydrogen peroxide and peroxynitrous acid is nearly five orders of magnitude lower.
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Affiliation(s)
- Matías N Möller
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias and Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo, Uruguay.
| | - Ana Denicola
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias and Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo, Uruguay.
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10
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Huang Y, Liu Y, Chen Y, Song M, Huang M, Xue J, Liu L, Li J. Probing the interactions of phthalocyanine-based photosensitizers with model phospholipid bilayer by molecular dynamics simulations. J PORPHYR PHTHALOCYA 2018. [DOI: 10.1142/s1088424618500566] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Phthalocyanines (Pc) have received considerable attention in the design of photosensitizers for photodynamic therapy (PDT). It is of great interest to design novel Pc-based photosensitizer with improved biological efficiency, which largely relies on the understanding of the interactions of Pc with cell membranes at a molecular level. Here, via all-atom molecular dynamics simulations, we explored the interaction mechanism between a model phospholipid bilayer and three zinc Pc (ZnPc) molecules with different hydrophobicity in nature. We find that the adsorption and insertion behaviors of ZnPc molecules in the model bilayer are different due to the differing hydrophobicity and interaction patterns with phospholipids. Moreover, our simulations demonstrate that the conjunction of a ZnPc skeleton with a cholesterol moiety may reduce the intrinsic molecular rotation of ZnPc in membranes, presumably leading to an increase of the generation efficiency of reactive oxygen species for PDT. The molecular insights obtained here are likely to help improve the rational design of novel photosensitizers with enhanced cellular uptake and photocytotoxic activity.
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Affiliation(s)
- Yuchao Huang
- National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Yichang Liu
- National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Yayu Chen
- National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Meiru Song
- National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Mingdong Huang
- National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Jinping Xue
- National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Lin Liu
- National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Jinyu Li
- National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
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11
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M Cordeiro R. Reactive Oxygen and Nitrogen Species at Phospholipid Bilayers: Peroxynitrous Acid and Its Homolysis Products. J Phys Chem B 2018; 122:8211-8219. [PMID: 30078319 DOI: 10.1021/acs.jpcb.8b07158] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peroxynitrite is a powerful and long-lived oxidant generated in vivo. Peroxynitrous acid (ONOOH), its protonated form, may penetrate into phospholipid bilayers and undergo homolytic cleavage to nitrogen dioxide (·NO2) and hydroxyl radicals (·OH), causing severe nitro-oxidative damage. The membrane environment is thought to influence ONOOH reactions, but the mechanisms remain speculative. Most experimental techniques lack the level of resolution required to keep track of the motion of very reactive species and their interactions with the membrane. Here, we performed molecular dynamics simulations of the permeation, interactions, and dynamics of ONOOH and its homolysis products in the phospholipid membrane environment. We started by developing an ONOOH model that successfully accounted for its conformational equilibria and solvation energies. Membrane permeation of ONOOH was accompanied by conformational changes. ONOOH exhibited a strong tendency to bind to and accumulate at the membrane headgroup region. There, ONOOH homolysis led to ·NO2 radicals, which in turn partitioned to the membrane interior. About one-third of the ·OH radicals readily escaped to the aqueous phase within 1 ns. However, a significant number of ·OH radicals became trapped at the lipid headgroup region for a longer period. The possible implications for membrane-based nitration and oxidation processes were discussed.
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Affiliation(s)
- Rodrigo M Cordeiro
- Centro de Ciências Naturais e Humanas , Universidade Federal do ABC , Avenida dos Estados 5001 , CEP 09210-580 Santo André , São Paulo , Brazil
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12
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Dotson RJ, Pias SC. Reduced Oxygen Permeability upon Protein Incorporation Within Phospholipid Bilayers. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1072:405-411. [PMID: 30178379 DOI: 10.1007/978-3-319-91287-5_65] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Intracellular oxygenation is key to energy metabolism as well as tumor radiation therapy. Although integral proteins are ubiquitous in membranes, few studies have considered their effects on molecular oxygen permeability. Published experimental work with rhodopsin and bacteriorhodopsin has led to the hypothesis that integral proteins lessen membrane oxygen permeability, as well as the permeability of the lipid region. The current work uses atomistic molecular dynamics simulations to test the influence of an ungated potassium channel protein on the oxygen permeability of palmitoyloleoylphosphatidylcholine (POPC) bilayers with and without cholesterol. Consistent with experiment, whole-membrane oxygen permeability is cut in half upon adding 30 wt% potassium channel protein to POPC, and the apparent permeability of the lipid portion of the membrane decreases by 40%. Unexpectedly, oxygen is found to interact directly with the protein surface, accompanied by a 40% reduction of the apparent whole-membrane diffusion coefficient. Similar effects are seen in systems combining the potassium channel with 1:1 POPC/cholesterol, but the magnitude of permeability reduction is smaller by ~30%. Overall, the simulations indicate that integral proteins can reduce oxygen permeability by altering the diffusional path and the local diffusivity. This effect may be especially important in the protein-dense membranes of mitochondria.
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Affiliation(s)
- Rachel J Dotson
- Department of Chemistry, New Mexico Institute of Mining and Technology (New Mexico Tech), Socorro, NM, USA
| | - Sally C Pias
- Department of Chemistry, New Mexico Institute of Mining and Technology (New Mexico Tech), Socorro, NM, USA.
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13
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Galstyan A, Putze J, Dobrindt U. Gaining Access to Bacteria through (Reversible) Control of Lipophilicity. Chemistry 2017; 24:1178-1186. [DOI: 10.1002/chem.201704562] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Indexed: 01/21/2023]
Affiliation(s)
- Anzhela Galstyan
- Center for Nanotechnology; Physikalisches Institut; Westfälische Wilhelms-Universität Münster; Heisenbergstrasse 11 48149 Münster Germany
| | - Johannes Putze
- Institut für Hygiene; Westfälische Wilhelms-Universität Münster; Mendelstraße 7 48149 Münster Germany
| | - Ulrich Dobrindt
- Institut für Hygiene; Westfälische Wilhelms-Universität Münster; Mendelstraße 7 48149 Münster Germany
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14
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Plesnar E, Szczelina R, Subczynski WK, Pasenkiewicz-Gierula M. Is the cholesterol bilayer domain a barrier to oxygen transport into the eye lens? BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:434-441. [PMID: 29079282 DOI: 10.1016/j.bbamem.2017.10.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/20/2017] [Accepted: 10/23/2017] [Indexed: 11/16/2022]
Abstract
In the eye lens, the oxygen partial pressure is very low and the cholesterol (Chol) content in cell membranes is very high. Disturbance of these quantities results in cataract development. In human lens membranes, both bulk phospholipid-Chol domains and the pure Chol bilayer domains (CBDs) were experimentally detected. It is hypothesized that the CBD constitutes a significant barrier to oxygen transport into the lens. Transmembrane profiles of the oxygen diffusion-concentration product, obtained with electron paramagnetic resonance spin-labeling methods, allow evaluation of the oxygen permeability (PM) of phospholipid membranes but not the CBD. Molecular dynamics simulation can independently provide components of the product across any bilayer domain, thus allowing evaluation of the PM across the CBD. Therefore, to test the hypothesis, MD simulation was used. Three bilayers containing palmitoyl-oleoyl-phosphorylcholine (POPC) and Chol were built. The pure Chol bilayer modeled the CBD, the 1:1 POPC-Chol bilayer modeled the bulk membrane in which the CBD is embedded, and the POPC bilayer was a reference. To each model, 200 oxygen molecules were added. After equilibration, the oxygen concentration and diffusion profiles were calculated for each model and multiplied by each other. From the respective product profiles, the PM of each bilayer was calculated. Favorable comparison with experimental data available only for the POPC and POPC-Chol bilayers validated these bilayer models and allowed the conclusion that oxygen permeation across the CBD is ~10 smaller than across the bulk membrane, supporting the hypothesis that the CBD is a barrier to oxygen transport into the eye lens.
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Affiliation(s)
- Elzbieta Plesnar
- Department of Computational Biophysics and Bioinformatics, WBBiB, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland.
| | - Robert Szczelina
- Department of Bioinformatics, MCB, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland.
| | - Witold K Subczynski
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
| | - Marta Pasenkiewicz-Gierula
- Department of Computational Biophysics and Bioinformatics, WBBiB, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland.
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15
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Influence of Cholesterol on the Oxygen Permeability of Membranes: Insight from Atomistic Simulations. Biophys J 2017; 112:2336-2347. [PMID: 28591606 PMCID: PMC5474842 DOI: 10.1016/j.bpj.2017.04.046] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 04/26/2017] [Accepted: 04/28/2017] [Indexed: 12/31/2022] Open
Abstract
Cholesterol is widely known to alter the physical properties and permeability of membranes. Several prior works have implicated cell membrane cholesterol as a barrier to tissue oxygenation, yet a good deal remains to be explained with regard to the mechanism and magnitude of the effect. We use molecular dynamics simulations to provide atomic-resolution insight into the influence of cholesterol on oxygen diffusion across and within the membrane. Our simulations show strong overall agreement with published experimental data, reproducing the shapes of experimental oximetry curves with high accuracy. We calculate the upper-limit transmembrane oxygen permeability of a 1-palmitoyl,2-oleoylphosphatidylcholine phospholipid bilayer to be 52 ± 2 cm/s, close to the permeability of a water layer of the same thickness. With addition of cholesterol, the permeability decreases somewhat, reaching 40 ± 2 cm/s at the near-saturating level of 62.5 mol % cholesterol and 10 ± 2 cm/s in a 100% cholesterol mimic of the experimentally observed noncrystalline cholesterol bilayer domain. These reductions in permeability can only be biologically consequential in contexts where the diffusional path of oxygen is not water dominated. In our simulations, cholesterol reduces the overall solubility of oxygen within the membrane but enhances the oxygen transport parameter (solubility-diffusion product) near the membrane center. Given relatively low barriers to passing from membrane to membrane, our findings support hydrophobic channeling within membranes as a means of cellular and tissue-level oxygen transport. In such a membrane-dominated diffusional scheme, the influence of cholesterol on oxygen permeability is large enough to warrant further attention.
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Bettanin F, Jurinovich S, Caprasecca S, Mennucci B, Homem-de-Mello P. A quantum chemical investigation of the solvatochromism of a phthalocyanine within a lipid bilayer: Comparison between continuum and atomistic models. J Photochem Photobiol A Chem 2017. [DOI: 10.1016/j.jphotochem.2017.04.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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17
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Ghysels A, Venable RM, Pastor RW, Hummer G. Position-Dependent Diffusion Tensors in Anisotropic Media from Simulation: Oxygen Transport in and through Membranes. J Chem Theory Comput 2017; 13:2962-2976. [PMID: 28482659 DOI: 10.1021/acs.jctc.7b00039] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A Bayesian-based methodology is developed to estimate diffusion tensors from molecular dynamics simulations of permeants in anisotropic media, and is applied to oxygen in lipid bilayers. By a separation of variables in the Smoluchowski diffusion equation, the multidimensional diffusion is reduced to coupled one-dimensional diffusion problems that are treated by discretization. The resulting diffusivity profiles characterize the membrane transport dynamics as a function of the position across the membrane, discriminating between diffusion normal and parallel to the membrane. The methodology is first validated with neat water, neat hexadecane, and a hexadecane slab surrounded by water, the latter being a simple model for a lipid membrane. Next, a bilayer consisting of pure 1-palmitoyl 2-oleoylphosphatidylcholine (POPC), and a bilayer mimicking the lipid composition of the inner mitochondrial membrane, including cardiolipin, are investigated. We analyze the detailed time evolution of oxygen molecules, in terms of both normal diffusion through and radial diffusion inside the membrane. Diffusion is fast in the more loosely packed interleaflet region, and anisotropic, with oxygen spreading more rapidly in the membrane plane than normal to it. Visualization of the propagator shows that oxygen enters the membrane rapidly, reaching its thermodynamically favored center in about 1 ns, despite the free energy barrier at the headgroup region. Oxygen transport is quantified by computing the oxygen permeability of the membranes and the average radial diffusivity, which confirm the anisotropy of the diffusion. The position-dependent diffusion constants and free energies are used to construct compartmental models and test assumptions used in estimating permeability, including Overton's rule. In particular, a hexadecane slab surrounded by water is found to be a poor model of oxygen transport in membranes because the relevant energy barriers differ substantially.
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Affiliation(s)
- An Ghysels
- Center for Molecular Modeling, Ghent University , Technologiepark 903, Zwijnaarde 9052, Belgium
| | - Richard M Venable
- Laboratory of Computational Biology, National Heart Lung Blood Institute, National Institutes of Health , Bethesda, Maryland 20824, United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart Lung Blood Institute, National Institutes of Health , Bethesda, Maryland 20824, United States
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics and Institute for Biophysics, Goethe University Frankfurt , Frankfurt am Main 60438, Germany
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18
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Cometto FP, Ruano G, Soria FA, Calderón CA, Paredes-Olivera PA, Zampieri G, Patrito EM. Thermal and Chemical Stability of n -Hexadecanethiol Monolayers on Au(111) in O 2 Environments. Electrochim Acta 2016. [DOI: 10.1016/j.electacta.2016.08.119] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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19
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Möller MN, Li Q, Chinnaraj M, Cheung HC, Lancaster JR, Denicola A. Solubility and diffusion of oxygen in phospholipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2923-2930. [PMID: 27614191 DOI: 10.1016/j.bbamem.2016.09.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 07/15/2016] [Accepted: 09/06/2016] [Indexed: 11/16/2022]
Abstract
The transport of oxygen and other nonelectrolytes across lipid membranes is known to depend on both diffusion and solubility in the bilayer, and to be affected by changes in the physical state and by the lipid composition, especially the content of cholesterol and unsaturated fatty acids. However, it is not known how these factors affect diffusion and solubility separately. Herein we measured the partition coefficient of oxygen in liposome membranes of dilauroyl-, dimiristoyl- and dipalmitoylphosphatidylcholine in buffer at different temperatures using the equilibrium-shift method with electrochemical detection. The apparent diffusion coefficient was measured following the fluorescence quenching of 1-pyrenedodecanoate inserted in the liposome bilayers under the same conditions. The partition coefficient varied with the temperature and the physical state of the membrane, from below 1 in the gel state to above 2.8 in the liquid-crystalline state in DMPC and DPPC membranes. The partition coefficient was directly proportional to the partial molar volume and was then associated to the increase in free-volume in the membrane as a function of temperature. The apparent diffusion coefficients were corrected by the partition coefficients and found to be nearly the same, with a null dependence on viscosity and physical state of the membrane, probably because the pyrene is disturbing the surrounding lipids and thus becoming insensitive to changes in membrane viscosity. Combining our results with those of others, it is apparent that both solubility and diffusion increase when increasing the temperature or when comparing a membrane in the gel to one in the fluid state.
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Affiliation(s)
- Matías N Möller
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, and Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo, Uruguay.
| | - Qian Li
- Department of Anesthesiology, Center for Free Radical Biology, The University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Mathivanan Chinnaraj
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Herbert C Cheung
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Jack R Lancaster
- Departments of Pharmacology and Chemical Biology, Medicine, and Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Ana Denicola
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, and Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo, Uruguay.
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20
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Awoonor-Williams E, Rowley CN. Molecular simulation of nonfacilitated membrane permeation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:1672-87. [PMID: 26706099 DOI: 10.1016/j.bbamem.2015.12.014] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/05/2015] [Accepted: 12/09/2015] [Indexed: 12/29/2022]
Abstract
This is a review. Non-electrolytic compounds typically cross cell membranes by passive diffusion. The rate of permeation is dependent on the chemical properties of the solute and the composition of the lipid bilayer membrane. Predicting the permeability coefficient of a solute is important in pharmaceutical chemistry and toxicology. Molecular simulation has proven to be a valuable tool for modeling permeation of solutes through a lipid bilayer. In particular, the solubility-diffusion model has allowed for the quantitative calculation of permeability coefficients. The underlying theory and computational methods used to calculate membrane permeability are reviewed. We also discuss applications of these methods to examine the permeability of solutes and the effect of membrane composition on permeability. The application of coarse grain and polarizable models is discussed. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- Ernest Awoonor-Williams
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL, A1B 3X7 Canada
| | - Christopher N Rowley
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL, A1B 3X7 Canada.
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21
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Alvares R, Gupta S, Macdonald PM, Prosser RS. Temperature and Pressure Based NMR Studies of Detergent Micelle Phase Equilibria. J Phys Chem B 2014; 118:5698-706. [DOI: 10.1021/jp500139p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Rohan Alvares
- Department
of Chemistry, University of Toronto, UTM Campus, 3359 Mississauga
Road North, Mississauga, Ontario, Canada L5L 1C6
| | - Shaan Gupta
- Department
of Chemistry, University of Toronto, UTM Campus, 3359 Mississauga
Road North, Mississauga, Ontario, Canada L5L 1C6
| | - Peter M. Macdonald
- Department
of Chemistry, University of Toronto, UTM Campus, 3359 Mississauga
Road North, Mississauga, Ontario, Canada L5L 1C6
| | - R. Scott Prosser
- Department
of Chemistry, University of Toronto, UTM Campus, 3359 Mississauga
Road North, Mississauga, Ontario, Canada L5L 1C6
- Department
of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
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22
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Dékány Fraňová M, Vattulainen I, Samuli Ollila O. Can pyrene probes be used to measure lateral pressure profiles of lipid membranes? Perspective through atomistic simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:1406-11. [DOI: 10.1016/j.bbamem.2014.01.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 01/07/2014] [Accepted: 01/30/2014] [Indexed: 10/25/2022]
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23
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Cordeiro RM. Reactive oxygen species at phospholipid bilayers: distribution, mobility and permeation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:438-44. [PMID: 24095673 DOI: 10.1016/j.bbamem.2013.09.016] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 09/12/2013] [Accepted: 09/23/2013] [Indexed: 10/26/2022]
Abstract
Reactive oxygen species (ROS) are involved in biochemical processes such as redox signaling, aging, carcinogenesis and neurodegeneration. Although biomembranes are targets for reactive oxygen species attack, little is known about the role of their specific interactions. Here, molecular dynamics simulations were employed to determine the distribution, mobility and residence times of various reactive oxygen species at the membrane-water interface. Simulations showed that molecular oxygen (O2) accumulated at the membrane interior. The applicability of this result to singlet oxygen ((1)O2) was discussed. Conversely, superoxide (O2(-)) radicals and hydrogen peroxide (H2O2) remained at the aqueous phase. Both hydroxyl (HO) and hydroperoxyl (HO2) radicals were able to penetrate deep into the lipid headgroups region. Due to membrane fluidity and disorder, these radicals had access to potential peroxidation sites along the lipid hydrocarbon chains, without having to overcome the permeation free energy barrier. Strikingly, HO2 radicals were an order of magnitude more concentrated in the headgroups region than in water, implying a large shift in the acid-base equilibrium between HO2 and O2(-). In comparison with O2, both HO and HO2 radicals had lower lateral mobility at the membrane. Simulations revealed that there were intermittent interruptions in the H-bond network around the HO radicals at the headgroups region. This effect is expected to be unfavorable for the H-transfer mechanism involved in HO diffusion. The implications for lipid peroxidation and for the effectiveness of membrane antioxidants were evaluated.
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Affiliation(s)
- Rodrigo M Cordeiro
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Rua Santa Adélia 166, CEP 09210-170, Santo André (SP), Brazil.
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24
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Cordeiro RM, Miotto R, Baptista MS. Photodynamic Efficiency of Cationic meso-Porphyrins at Lipid Bilayers: Insights from Molecular Dynamics Simulations. J Phys Chem B 2012; 116:14618-27. [DOI: 10.1021/jp308179h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Rodrigo M. Cordeiro
- Centro de
Ciências Naturais
e Humanas, Universidade Federal do ABC,
Rua Santa Adélia 166, CEP 09210-170, Santo André (SP),
Brazil
| | - Ronei Miotto
- Centro de
Ciências Naturais
e Humanas, Universidade Federal do ABC,
Rua Santa Adélia 166, CEP 09210-170, Santo André (SP),
Brazil
| | - Maurício S. Baptista
- Departamento
de
Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes
748, CEP 05508-900, São Paulo (SP), Brazil
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25
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Kitevski-LeBlanc JL, Prosser RS. Current applications of 19F NMR to studies of protein structure and dynamics. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2012; 62:1-33. [PMID: 22364614 DOI: 10.1016/j.pnmrs.2011.06.003] [Citation(s) in RCA: 210] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 07/01/2011] [Indexed: 05/20/2023]
Affiliation(s)
- Julianne L Kitevski-LeBlanc
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Rd., North Mississauga, Ontario, Canada
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26
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Al-Abdul-Wahid MS, Verardi R, Veglia G, Prosser RS. Topology and immersion depth of an integral membrane protein by paramagnetic rates from dissolved oxygen. JOURNAL OF BIOMOLECULAR NMR 2011; 51:173-183. [PMID: 21947925 DOI: 10.1007/s10858-011-9551-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2011] [Accepted: 06/30/2011] [Indexed: 05/31/2023]
Abstract
In studies of membrane proteins, knowledge of protein topology can provide useful insight into both structure and function. In this work, we present a solution NMR method for the measurement the tilt angle and average immersion depth of alpha helices in membrane proteins, from analysis of the paramagnetic relaxation rate enhancements arising from dissolved oxygen. No modification to the micelle or protein is necessary, and the topology of both transmembrane and amphipathic helices are readily determined. We apply this method to the measure the topology of a monomeric mutant of phospholamban (AFA-PLN), a 52-residue membrane protein containing both an amphipathic and a transmembrane alpha helix. In dodecylphosphocholine micelles, the amphipathic helix of AFA-PLN was found to have a tilt angle of 87° ± 1° and an average immersion depth of 13.2 Å. The transmembrane helix was found to have an average immersion depth of 5.4 Å, indicating residues 41 and 42 are closest to the micelle centre. The resolution of paramagnetic relaxation rate enhancements from dissolved oxygen compares favourably to those from Ni (II), a hydrophilic paramagnetic species.
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27
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Al-Abdul-Wahid MS, Evanics F, Prosser RS. Dioxygen transmembrane distributions and partitioning thermodynamics in lipid bilayers and micelles. Biochemistry 2011; 50:3975-83. [PMID: 21510612 DOI: 10.1021/bi200168n] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cellular respiration, mediated by the passive diffusion of oxygen across lipid membranes, is key to many basic cellular processes. In this work, we report the detailed distribution of oxygen across lipid bilayers and examine the thermodynamics of oxygen partitioning via NMR studies of lipids in a small unilamellar vesicle (SUV) morphology. Dissolved oxygen gives rise to paramagnetic chemical shift perturbations and relaxation rate enhancements, both of which report on local oxygen concentration. From SUVs containing the phospholipid sn-2-perdeuterio-1-myristelaidoyl, 2-myristoyl-sn-glycero-3-phosphocholine (MLMPC), an analogue of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), we deduced the complete trans-bilayer oxygen distribution by measuring (13)C paramagnetic chemical shifts perturbations for 18 different sites on MLMPC arising from oxygen at a partial pressure of 30 bar. The overall oxygen solubility at 45 °C spans a factor of 7 between the bulk water (23.7 mM) and the bilayer center (170 mM) and is lowest in the vicinity of the phosphocholine headgroup, suggesting that oxygen diffusion across the glycerol backbone should be the rate-limiting step in diffusion-mediated passive transport of oxygen across the lipid bilayer. Lowering of the temperature from 45 to 25 °C gave rise to a slight decrease of the oxygen solubility within the hydrocarbon interior of the membrane. An analysis of the temperature dependence of the oxygen solubility profile, as measured by (1)H paramagnetic relaxation rate enhancements, reveals that oxygen partitioning into the bilayer is entropically favored (ΔS° = 54 ± 3 J K(-1) mol(-1)) and must overcome an enthalpic barrier (ΔH° = 12.0 ± 0.9 kJ mol(-1)).
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Affiliation(s)
- M Sameer Al-Abdul-Wahid
- Department of Chemistry, University of Toronto, UTM, North Mississauga, Ontario, Canada L5L 1C6
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28
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Hu SQ, Guo AL, Yan YG, Jia XL, Geng YF, Guo WY. Computer simulation of diffusion of corrosive particle in corrosion inhibitor membrane. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2010.12.019] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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29
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Al-Abdul-Wahid MS, Neale C, Pomès R, Prosser RS. A solution NMR approach to the measurement of amphiphile immersion depth and orientation in membrane model systems. J Am Chem Soc 2009; 131:6452-9. [PMID: 19415935 DOI: 10.1021/ja808964e] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oxygen and Ni(II) are ideal paramagnetic species for NMR studies of immersion depth since they establish prominent concentration gradients across the membrane-water interface of either bilayers or micelles. Corresponding gradients of paramagnetic shifts and relaxation rates are observed by NMR for membrane embedded amphiphiles. Specifically, upon dissolution of oxygen at a partial pressure of 20 bar or more, (13)C NMR spectra of membrane embedded amphiphiles reveal chemical shift perturbations which depend sensitively on average immersion depth in the membrane. Similarly, depth-dependent enhancements of spin-lattice relaxation rates can be detected by (1)H NMR. Generally, such paramagnetic effects depend both on steric or accessibility factors and on the local concentration of the paramagnet. The steric terms can be factored out by combining paramagnetic rates arising from O(2) and Ni, in the form of a ratio, R(1P)(O(2))/R(1P)(Ni). The natural logarithm of this ratio is shown to depend linearly on immersion depth in a micelle. The analysis is verified using molecular dynamics simulations of dodecylphosphocholine in a detergent micelle, while thorough consideration of the paramagnetic rate data also allows for the determination of the orientation of imipramine in the micelle. Thus, a complete picture of topology arises from this approach which is readily applicable to studies of drugs and amphiphiles in fast-tumbling bicelles, small unilamellar vesicles, and micelles.
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Affiliation(s)
- M Sameer Al-Abdul-Wahid
- Department of Chemistry, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, Ontario, Canada, L5L 1C6
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30
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Li X, Rinkevicius Z, Tu Y, Tian H, Ågren H. Paramagnetic Perturbation of the 19F NMR Chemical Shift in Fluorinated Cysteine by O2: A Theoretical Study. J Phys Chem B 2009; 113:10916-22. [DOI: 10.1021/jp902659s] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xin Li
- Department of Theoretical Chemistry, Royal Institute of Technology, AlbaNova University Center, S-106 91 Stockholm, Sweden, Laboratory for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, Shanghai 200237, People’s Republic of China, and Biophysical Chemistry, School of Science and Technology, Örebro University, 701 82 Örebro, Sweden
| | - Zilvinas Rinkevicius
- Department of Theoretical Chemistry, Royal Institute of Technology, AlbaNova University Center, S-106 91 Stockholm, Sweden, Laboratory for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, Shanghai 200237, People’s Republic of China, and Biophysical Chemistry, School of Science and Technology, Örebro University, 701 82 Örebro, Sweden
| | - Yaoquan Tu
- Department of Theoretical Chemistry, Royal Institute of Technology, AlbaNova University Center, S-106 91 Stockholm, Sweden, Laboratory for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, Shanghai 200237, People’s Republic of China, and Biophysical Chemistry, School of Science and Technology, Örebro University, 701 82 Örebro, Sweden
| | - He Tian
- Department of Theoretical Chemistry, Royal Institute of Technology, AlbaNova University Center, S-106 91 Stockholm, Sweden, Laboratory for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, Shanghai 200237, People’s Republic of China, and Biophysical Chemistry, School of Science and Technology, Örebro University, 701 82 Örebro, Sweden
| | - Hans Ågren
- Department of Theoretical Chemistry, Royal Institute of Technology, AlbaNova University Center, S-106 91 Stockholm, Sweden, Laboratory for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, Shanghai 200237, People’s Republic of China, and Biophysical Chemistry, School of Science and Technology, Örebro University, 701 82 Örebro, Sweden
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31
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An NMR method for the determination of protein binding interfaces using TEMPOL-induced chemical shift perturbations. Biochim Biophys Acta Gen Subj 2009; 1790:1368-76. [PMID: 19520148 DOI: 10.1016/j.bbagen.2009.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Revised: 05/28/2009] [Accepted: 06/01/2009] [Indexed: 11/20/2022]
Abstract
BACKGROUND The determination of protein-protein interfaces is of crucial importance to understand protein function and to guide the design of compounds. To identify protein-protein interface by NMR spectroscopy, 13C NMR paramagnetic shifts induced by freely diffusing 4-hydroxy-2, 2, 6, 6-tetramethyl-piperidine-1-oxyl (TEMPOL) are promising, because TEMPOL affects distinct 13C NMR chemical shifts of the solvent accessible nuclei belonging to proteins of interest, while 13C nuclei within the interior of the proteins may be distinguished by a lack of such shifts. METHOD We measured the 13C NMR paramagnetic shifts induced by TEMPOL by recording 13C-(13)C TOCSY spectra for ubiquitin in the free state and the complex state with yeast ubiquitin hydrolase1 (YUH1). RESULTS Upon complexation of ubiquitin with YUH1, 13C NMR paramagnetic shifts associated with the protein binding interface were reduced by 0.05 ppm or more. The identified interfacial atoms agreed with the prior X-ray crystallographic data. CONCLUSIONS The TEMPOL-induced 13C chemical shift perturbation is useful to determine precise protein-protein interfaces. GENERAL SIGNIFICANCE The present method is a useful method to determine protein-protein interface by NMR, because it has advantages in easy sample preparations, simple data analyses, and wide applicabilities.
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32
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CRISOSTOMO ANAG, MORENO RAPHAELB, NAVARATNAM SUPPIAH, WILKINSON JAMESA, BISBY ROGERH. Generation of superoxide and singlet oxygen from alpha-tocopherolquinone and analogues. Free Radic Res 2007; 41:730-7. [PMID: 17516246 PMCID: PMC2080821 DOI: 10.1080/10715760701324075] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Three potential routes to generation of reactive oxygen species (ROS) from alpha-tocopherolquinone (alpha-TQ) have been identified. The quinone of the water-soluble vitamin E analogue Trolox C (Trol-Q) is reduced by hydrated electron and isopropanol alpha-hydroxyalkyl radical, and the resulting semiquinone reacts with molecular oxygen to form superoxide with a second order rate constant of 1.3 x 10(8) dm(3)/mol/s, illustrating the potential for redox cycling. Illumination (UV-A, 355 nm) of the quinone of 2,2,5,7,8-pentamethyl-6-hydroxychromanol (PMHC-Q) leads to a reactive short-lived (ca. 10(- 6) s) triplet state, able to oxidise tryptophan with a second order rate constant greater than 10(9) dm(3)/mol/s. The triplet states of these quinones sensitize singlet oxygen formation with quantum yields of about 0.8. Such potentially damaging reactions of alpha-TQ may in part account for the recent findings that high levels of dietary vitamin E supplementation lack any beneficial effect and may lead to slightly enhanced levels of overall mortality.
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Affiliation(s)
- ANA G CRISOSTOMO
- Biomedical Sciences Research Institute, University of Salford, Salford M5 4WT, UK
| | - RAPHAEL B MORENO
- Biomedical Sciences Research Institute, University of Salford, Salford M5 4WT, UK
| | - SUPPIAH NAVARATNAM
- Biomedical Sciences Research Institute, University of Salford, Salford M5 4WT, UK
- FRRF, CCLRC Daresbury Laboratory, Warrington WA4 4AD, UK
| | - JAMES A WILKINSON
- Biomedical Sciences Research Institute, University of Salford, Salford M5 4WT, UK
| | - ROGER H BISBY
- Biomedical Sciences Research Institute, University of Salford, Salford M5 4WT, UK
- Correspondence: Roger Bisby, Biomedical Sciences Research Institute, Peel Building, University of Salford, Salford M5 4WT, UK. Fax 0161 295 5015. Email
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